A Proposal for Dynamic Access Lists for TCP/IP Packet Filering

The use of IP filtering to improve system security is well established, and although limited in what it can achieve has proved to be efficient and effective. In the design of a security policy there is always a trade-off between usability and security. Restricting access means that legitimate use of the network is prevented; allowing access means illegitimate use may be allowed. Static access list make finding a balance particularly stark -- we pay the price of decreased security 100% of the time even if the benefit of increased usability is only gained 1% of the time. Dynamic access lists would allow the rules to change for short periods of time, and to allow local changes by non-experts. The network administrator can set basic security guide-lines which allow certain basic services only. All other services are restricted, but users are able to request temporary exceptions in order to allow additional access to the network. These exceptions are granted depending on the privileges of the user. This paper covers the following topics: (1) basic introduction to TCP/IP filtering; (2) semantics for dynamic access lists and; (3) a proposed protocol for allowing dynamic access; and (4) a method for representing access lists so that dynamic update and look-up can be done efficiently performed.Comment: 12 pages. Shortened version appeared in SAICSIT 200

An overview of the wcd EST clustering tool

Summary: The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d 2 distance function or edit distance, improving existing implementations of d 2. It supports merging, refinement and reclustering of clusters. It is ‘drop in’ compatible with the StackPack clustering package. wcd supports parallelization under both shared memory and cluster architectures. It is distributed with an EMBOSS wrapper allowing wcd to be installed as part of an EMBOSS installation (and so provided by a web server)

Resource sharing across heterogenous networks

Sharing resources on a computer network, especially in heterogeneous environments, has m any benefits: new applications become possible, and use of technology cheaper. This dissertation investigates how resources— in particular printing resources—may b e shared. While still incomplete, an existing theoretical framework for data communication and resource sharing, the ISO-051 Reference Model, provides useful background information and tools for analysis. A discussion o f this framework complements a survey o f the principles and current state of file and printer servers, and distributed systems. An analysis of the design and implementation of a printer server acting as a b ridge between two networks illustrates problem s and results found in distributed system s generally. The dissertation concludes by analyzing the strengths and shortcomings of the Reference Model and distributed systems. This and developments in technology lead to a proposal of an extended model for printer services, and clarification of printer servers' needs and requirements

Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

<p>Abstract</p> <p>Background</p> <p>Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution.</p> <p>Results</p> <p>A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (<b><it>F</it></b>unctional <b><it>I</it></b>nference using the <b><it>R</it></b>ates of <b><it>E</it></b>volution), which aligns sequences using the evolutionary rate at codon sites, as measured by the <it>dN</it>/<it>dS </it>ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions). Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data) may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the method of choice in these cases.</p> <p>Conclusions</p> <p>FIRE provides proof of concept that it is possible to align sequences and infer domain function by using evolutionary rates rather than residue similarity. This represents a new approach to sequence analysis with a wide range of potential applications in molecular biology.</p

Fast packet filtering using N-ary decision diagrams

Abstrac

Establishing an academic biobank in a resource-challenged environment

Past practices of informal sample collections and spreadsheets for data and sample management fall short of best-practice models for biobanking, and are neither cost effective nor efficient to adequately serve the needs of large research studies. The biobank of the Sydney Brenner Institute for Molecular Bioscience serves as a bioresource for institutional, national and international research collaborations. It provides high-quality human biospecimens from African populations, secure data and sample curation and storage, as well as monitored sample handling and management processes, to promote both non-communicable and infectious-disease research. Best-practice guidelines have been adapted to align with a low-resource setting and have been instrumental in the development of a quality-management system, including standard operating procedures and a quality-control regimen. Here, we provide a summary of 10 important considerations for initiating and establishing an academic research biobank in a low-resource setting. These include addressing ethical, legal, technical, accreditation and/or certification concerns and financial sustainability

Building Infrastructure for African Human Genomic Data Management

Human genomic data are large and complex, and require adequate infrastructure for secure storage and transfer. The NIH and The Wellcome Trust have funded multiple projects on genomic research, including the Human Heredity and Health in Africa (H3Africa) initiative, and data are required to be deposited into the public domain. The European Genome-phenome Archive (EGA) is a repository for sequence and genotype data where the data access is controlled by access committees. Access is determined by a formal application procedure for the purpose of secure storage and distribution, and must be in line with the informed consent of the study participants. H3Africa researchers based in Africa and generating their own data can benefit tremendously from the data sharing capabilities of the internet by using the appropriate technologies. The H3Africa Data Archive is an effort between the H3Africa data generating projects, H3ABioNet and the EGA to store and submit genomic data to public repositories. H3ABioNet maintains the security of the H3Africa Data Archive, ensures ethical security compliance, supports users with data submission and facilitates the data transfer. The goal is to ensure efficient data flow between researchers, the archive and the EGA or other public repositories. To comply with the H3Africa data sharing and release policy, nine months after the data is in secure storage, H3ABioNet converts the data into an XML format ready for submission to EGA. This article describes the infrastructure that has been developed for African human genomic data management

Establishing an academic biobank in a resource-challenged environment

Past practices of informal sample collections and spreadsheets for data and sample management fall short of best-practice models for biobanking, and are neither cost effective nor efficient to adequately serve the needs of large research studies. The biobank of the Sydney Brenner Institute for Molecular Bioscience serves as a bioresource for institutional, national and international research collaborations. It provides high-quality human biospecimens from African populations, secure data and sample curation and storage, as well as monitored sample handling and management processes, to promote both non-communicable and infectious-disease research. Best-practice guidelines have been adapted to align with a low-resource setting and have been instrumental in the development of a quality-management system, including standard operating procedures and a quality-control regimen. Here, we provide a summary of 10 important considerations for initiating and establishing an academic research biobank in a low-resource setting. These include addressing ethical, legal, technical, accreditation and/or certification concerns and financial sustainability